Van Aert had a dream start to his first Tour de France, having worn the white jersey of best young rider for four stages and then winning the bunch sprint on stage 10.
He was running second at the second time check, 16 seconds behind Lotto Soudal's Thomas de Gendt and on track for a strong showing until he brushed up against the barriers in a turn inside the final kilometre and suffered an large gash to his thigh.
Medics treated the rider on the side of the course before Jumbo-Visma announced that Van Aert would not continue via Twitter.
The team later confirmed that Van Aert underwent surgery to repair the wound that penetrated into the muscle but he did not sustain any fractures.
Mathieu Heijboer, Jumbo-Visma's head of performance, explained the incident in a video on the team's web site.
"Wout was entering the final kilometre, and there was a very narrow corner and he rode close to the barriers. He hit one which caused him to crash. He suffered a very serious deep wound. It had to be surgically stitched," Heijboer said.
"It was a terrible sight. Wout saw his leg and he panicked. It was a horrific image. He immediately stood up and walked to the side. I told him 'sit down don't walk now'. I pulled the banner off the fence and put it over him so that he couldn't look at the wound. I said, 'don't look at it because it won't help'."
The barricade dug into Van Aert's hip, tearing into the skin, capsule and muscle of his upper thigh and hip. After being stabilised at the scene, he was taken to a hospital in Pau where surgeons stitched the wound closed.
"It took almost an hour," Heijboer said of the operation. "Wout is now in recovery. He'll go to the infirmary tonight and then remain in the hospital for a few days before he can go home."
The team did not make any predictions about when Van Aert would return to competition.
"I was supposed to be with Kruijswijk while he warmed up, but I couldn't leave Wout alone," Heijboer said. "There are a lot of emotions mixed together, but the fall of Wout overshadows everything."
Steven Kruijswijk had a strong ride in the time trial to move into third place in the overall standings, but also had mixed feelings. "After the fall of Wout I had to pick myself up again. This is such a shame, you don't wish this on anybody. I think I have done a great time trial, myself. The differences are small and I expect it will be an exciting Tour."